diff cutadapt_galaxy_wrapper.py @ 0:8b064ea16722

Initial version with multiple adapter support

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt_galaxy_wrapper.py	Fri May 13 15:54:01 2011 -0400
@@ -0,0 +1,131 @@
+#!/usr/bin/env python
+"""
+SYNOPSIS
+
+    cutadapt_galaxy_wrapper.py 
+        -i input_file
+        -o output_file
+        [-f format (fastq/fastq/etc.)]
+        [-a 3' adapter sequence]
+        [-b 3' or 5' anywhere adapter sequence]
+        [-e error_rate]
+        [-n count]
+        [-O overlap_length]
+        [--discard discard trimmed reads]
+        [-m minimum read length]
+        [-M maximum read length]
+        [-h,--help] [-v,--verbose] [--version]
+
+DESCRIPTION
+
+   Wrapper for cutadapt running as a galaxy tool
+
+AUTHOR
+
+    Lance Parsons <[e-mail]>
+
+LICENSE
+
+    This script is in the public domain, free from copyrights or restrictions.
+
+VERSION
+
+    $Id$
+"""
+
+import sys, os, traceback, optparse, shutil, subprocess, tempfile
+import re
+#from pexpect import run, spawn
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+def main ():
+
+    global options, args
+    # Setup Parameters 
+    params = []
+    if options.adapters != None:
+        params.append("-a %s" % " -a ".join(options.adapters))
+    if options.anywhere_adapters != None:
+        params.append("-b %s" % " -b ".join(options.anywhere_adapters))
+    if options.output_file != None:
+        params.append("-o %s" % options.output_file)
+    if options.error_rate != None:
+        params.append("-e %s" % options.error_rate)
+    if options.count != None:
+        params.append("-n %s" % options.count)
+    if options.overlap_length != None:
+        params.append("-O %s" % options.overlap_length)
+    if options.discard_trimmed:
+        params.append("--discard")
+    if options.minimum_length != None:
+        params.append("-m %s" % options.minimum_length)
+    if options.maximum_length != None:
+        params.append("-M %s" % options.maximum_length)
+
+    # cutadapt relies on the extension to determine file format: .fasta or .fastq
+    input_name = '.'.join((options.input,options.format))
+    # make temp directory
+    tmp_dir = tempfile.mkdtemp()
+
+    try:
+        # make a link to the input file in the tmp_dir
+        input_file = os.path.join(tmp_dir,os.path.basename(input_name)) 
+        os.symlink( options.input, input_file) 
+        
+        # generate commandline
+        cmd = 'cutadapt %s %s' % (' '.join(params),input_file)
+        proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir,
+                                stdout=subprocess.PIPE,
+                               stderr=subprocess.PIPE)
+        (stdoutdata, stderrdata) = proc.communicate()
+        returncode = proc.returncode
+        if returncode != 0:
+            raise Exception, 'Execution of cutadapt failed.\n%s' % stderrdata
+        print stderrdata
+
+    finally:
+        # clean up temp dir
+        if os.path.exists( input_name ):
+            os.remove( input_name )
+        if os.path.exists( tmp_dir ):
+            shutil.rmtree( tmp_dir )
+
+if __name__ == '__main__':
+    try:
+        parser = optparse.OptionParser(formatter=optparse.TitledHelpFormatter(), usage=globals()['__doc__'], version='$Id$')
+        parser.add_option( '-i', '--input', dest='input', help='The sequence input file' )
+        parser.add_option( '-f', '--format', dest='format', default='fastq',
+                          help='The sequence input file format (default: fastq)' )
+        parser.add_option ('-a', '--adapter', action='append', dest='adapters', help='3\' adapter sequence(s)')
+        parser.add_option ('-b', '--anywhere', action='append', dest='anywhere_adapters', help='5\' or 3\' "anywhere" adapter sequence(s)')
+        parser.add_option ('-e', '--error-rate', dest='error_rate', help='Maximum allowed error rate')
+        parser.add_option ('-n', '--times', dest='count', help='Try to remove adapters COUNT times')
+        parser.add_option ('-O', '--overlap', dest='overlap_length', help='Minimum overlap length')
+        parser.add_option ('--discard', '--discard-trimmed', dest='discard_trimmed', action='store_true', default=False, help='Discard reads that contain the adapter')
+        parser.add_option ('-m', '--minimum-length', dest='minimum_length', help='Discard reads that are shorter than LENGTH')
+        parser.add_option ('-M', '--maximum-length', dest='maximum_length', help='Discard reads that are longer than LENGTH')
+        parser.add_option ('-o', '--output', dest='output_file', help='The modified sequences are written to the file')
+        (options, args) = parser.parse_args()
+        if options.input == None:
+             stop_err("Misssing option --input")
+        if options.output_file == None:
+             stop_err("Misssing option --output")
+        if not os.path.exists(options.input):
+            stop_err("Unable to read intput file: %s" % options.input)
+   #if len(args) < 1:
+        #    parser.error ('missing argument')
+        main()
+        sys.exit(0)
+    except KeyboardInterrupt, e: # Ctrl-C
+        raise e
+    except SystemExit, e: # sys.exit()
+        raise e
+    except Exception, e:
+        print 'ERROR, UNEXPECTED EXCEPTION'
+        print str(e)
+        traceback.print_exc()
+        os._exit(1)
+